Adenylate kinase



Adenylate kinase (ADK) is a phosphotransferase which catalyzes the interconversion of ADP to ATP+AMP. ADK is important in cellular energy homeostasis. Dinucleotides polyphosphates like diadenosine pentaphosphate (AP5) inhibit ADK. The images at the left and at the right correspond to one representative ADK, i.e. the crystal structure of Adenylate kinase from Desulfovibrio gigas (3l0p).

 Adenylate kinase is an essential catalyst for cellular growth and multiplication. ADK belongs to a family of enzymes essential to life, and is highly abundant inside the cell. It is involved in the reversible transfer of the terminal phosphate group from Mg2+ATP to Mg2+AMP with high energy turnover: Mg2+ATP + AMP&#8596;Mg2+ADP + ADP.

Adenylate kinases (ADK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, three metal ions, zinc, cobalt and iron, have been found in ADK from Gram-negative bacteria. Crystal structures of substrate-free ADK from Desulfovibrio gigas with three different metal ions: Zn2+, Zn-ADK (2xb4); Co2+, Co-ADK (3l0s) and Fe2+, Fe-ADK (3l0p) bound in its LID domain have been determined by X-ray crystallography. All three crystal structures are very similar to each other with the same LID domain topology, the only change being the presence of the different metal atoms.

The structures of Zn-, Co- and Fe-ADK contain the characteristic LID domain (residues 125-163) and Core (residues 1-124 and 164-223) domains , which also include the AMP binding region. The LID domain harbors the Cys129-X5-His135-X15-Cys151-X2-Cys154- motif, which is responsible for metal binding in a tetrahedral fashion. In the absence of any substrate, the LID domain of all holo forms of ADK was present in a fully open conformational state. The Core domain is connected to the LID by residues 116-123 and 165-173. This Core domain mainly consists of a five stranded beta sheet surrounded by 5 helices that keep the integrity of the tertiary structure of the enzyme. A Walker motif with conserved sequence; G - X - X - G - X - G - K is present in the N-terminal region. The structures presented herein further reinforce the notion that the metal ion is purely structural, contributing to the stability of the LID domain.



3D Structures of Adenylate kinase
Update June 2011

ADK unliganded
4ake - EcADK - Escherichia coli

3gmt - ADK - Burkholderia pseudodomallei

3cm0 - ADK - Thermus thermophilus

2rh5 - AaADK - Aquifex aeolicus

1p4s - MtADK - Mycobacterium tuberculosis

2ar7 - hADK 4 - human

3ndp - hADK 4 (mutant)

1ki9 - ADK - Methanococcus thermolithotrophicus

1ak2, 2ak2 - bADK - bovine

3adk - ADK - pig

3be4 - CpADK – Cryptosporidium parvum

ADK mononucleotide complex
1ank - EcADK+AMP+AMPPNP

2cdn - MtADK+ADP

2bwj - hADK 5+AMP

1kht - ADK+AMP - Methanococcus voltae

1nks - ADK+AMP+ADP - Sulfolobus acidocaldarius

2ak3 - bADK+AMP

1dvr - yADK (mutant)+ATP analog - yeast

ADK complex with dinucletide polyphosphates
3hpq, 3hpr, 1e4v, 1e4y - EcADK (mutant)+AP5

1ake - EcADK+AP5

3h86 - ADK+AP5 - Methanococcus maripaludis

3fb4 - ADK+Zn+AP5 - Marinibacillus marinus

3dkv, 3dl0, 1p3j - BsADK+Zn+AP5 - Bacillus subtilis

2qaj, 2oo7, 2p3s, 2ori, 2osb, 2eu8 - BsADK (mutant)+Zn+AP5

2rgx - AaADK+Zn+AP5

][[3be4] - CpADK+AP5

2c9y - hADK 2+bis-adenosine tetraphosphate

2bbw - hADK 4+GP5

1s3g - ADK+Zn+AP5 - Bacillus globisporus

1zak - ADK+AP5 - maize

1zip, 1zin - ADK+Zn+Mn+AP5 - Bacillus stearothermophilus

1aky, 2aky - yADK+AP5

3aky - yADK (mutant)+AP5

ADK complexes with ions
3l0p - DgADK+Fe - Desulfovibrio gigas

3l0s - DgADK+Co

2xb4 - DgADK+Zn